I previously had XNA Game Connect installed long ago. I recently had to get another console (RRoD) to replace my old one. So, when I tried to run it again. it didn't want to connect. So I deleted my 360 in Device Center and followed the steps here (http://msdn.microsoft.com/en-us/library/bb975643.aspx) to connect my new 360 to my PC. This includes re-downloading the XNA Game Connect App.

Here's the problem I have this message that displays just below XNA Game Connect in the game selection list now. It says:
Registered to another console

It shouldn't make a difference. At least I hope not. But, the question I do have, can I register a second console?

When you run the newest download of game studio connect and it is in the 'waiting for connection' screen, have you tried pressing 'Y' to reset all connections? it will generate a new key for use between your new console and your dev PC.

I havent had use a new console yet so i havent come across this message, but maybe this helps

I've got two consoles registered and it doesn't seem to cause any problems, so long as I'm signed in with my Gamertag when using Connect on the Xbox that I didn't originally download it on.

I'm fairly sure Connect doesn't even fire up if you're not signed in, ut if it does, check you're signed in and connected to Xbox Live.

If you need to use your console offline, you may need to use the licence transfer tool to transfer your Connect licence from the old console to the new one, I assume it works the same as DLC.